GREMLIN.BAKERLAB.org

Archive: 2012 - 2013
SnoaL_3 - SnoaL-like domain
Pfam: PF13474 (v27) Consensus Sequence
Download Alignment
(Note: includes all positions in family; we filtered this alignment to remove sites that had > 75% gaps before running GREMLIN. )
Clan: CL0051
Length: 121
Sequences: 8858
Seq/Len: 73.21
HH_delta: 0.031 (20Jul13)
GREMLIN Results:
Residue pairs sorted by strength in covariance:

Legend: The darker and larger the blue dots, the higher strength in covariance. Below we provide the list of the top [1.5 x length] gremlin predictions, sequence seperation > 3. The i and j are positions as given in the consensus sequence. Show Scaled Distribution

ij Raw Score Scaled Score
16_D19_A1.94863.734
21_L46_R1.455532.789
28_F45_I1.273322.440
103_R112_V1.192852.286
26_D42_R1.186872.275
41_G44_A1.146632.197
10_E14_R1.12222.151
81_F96_G1.084552.079
79_G98_A1.073322.057
11_A19_A1.046352.005
25_S112_V1.046142.005
24_F28_F0.997161.911
19_A22_S0.928461.779
29_V113_H0.905081.735
7_E19_A0.896081.717
46_R50_E0.877521.682
77_V102_F0.862621.653
17_I21_L0.853551.636
18_D46_R0.852431.634
21_L42_R0.839851.610
25_S105_E0.831421.593
101_V113_H0.823621.578
7_E23_L0.810871.554
74_V103_R0.793151.520
76_V101_V0.792241.518
4_L102_F0.738451.415
47_A51_R0.730491.400
62_E82_R0.713131.367
79_G100_F0.700011.342
65_D80_E0.679261.302
73_D104_K0.675651.295
13_E61_I0.6711.286
43_E47_A0.669721.283
11_A23_L0.661141.267
43_E46_R0.64841.243
25_S110_K0.633361.214
44_A47_A0.629051.206
74_V101_V0.620521.189
70_V75_A0.616351.181
17_I50_E0.610371.170
47_A50_E0.603451.156
105_E110_K0.598841.148
40_R44_A0.590451.132
18_D21_L0.589621.130
29_V40_R0.588561.128
50_E54_E0.586451.124
24_F45_I0.577531.107
8_W20_L0.575851.104
7_E11_A0.575781.103
6_E10_E0.562911.079
11_A16_D0.540661.036
78_T99_T0.540651.036
82_R95_R0.533961.023
39_W44_A0.53081.017
42_R46_R0.530651.017
12_F20_L0.527421.011
8_W23_L0.526141.008
64_E80_E0.511940.981
8_W24_F0.511230.980
41_G45_I0.5110.979
15_G53_F0.510350.978
71_S74_V0.505590.969
80_E97_R0.494110.947
67_Q78_T0.483970.928
31_F38_I0.483220.926
102_F111_I0.481360.923
76_V99_T0.48030.920
105_E112_V0.475630.912
5_L102_F0.475570.911
84_R93_E0.474660.910
82_R93_E0.474020.908
51_R54_E0.468810.898
45_I49_F0.461350.884
4_L7_E0.45950.881
13_E60_S0.456660.875
69_S76_V0.453680.869
100_F111_I0.449870.862
81_F98_A0.445950.855
9_I13_E0.444840.853
31_F113_H0.443310.850
99_T113_H0.440050.843
27_D112_V0.439390.842
4_L23_L0.438820.841
83_L96_G0.435960.836
4_L111_I0.431470.827
80_E95_R0.424440.813
10_E13_E0.419590.804
4_L104_K0.418890.803
66_V79_G0.415360.796
78_T97_R0.410510.787
20_L49_F0.408080.782
11_A22_S0.407890.782
21_L43_E0.395690.758
5_L100_F0.39010.748
17_I46_R0.388030.744
18_D22_S0.387080.742
24_F30_F0.385290.738
7_E10_E0.380660.730
29_V38_I0.376130.721
7_E22_S0.371970.713
16_D22_S0.370720.710
5_L77_V0.369970.709
68_V77_V0.369950.709
25_S103_R0.368180.706
73_D103_R0.366890.703
18_D50_E0.357110.684
32_G98_A0.356930.684
12_F61_I0.349290.669
6_E66_V0.349260.669
11_A14_R0.349190.669
79_G83_L0.348970.669
64_E82_R0.344070.659
6_E9_I0.342410.656
34_G37_E0.341310.654
77_V100_F0.335480.643
27_D105_E0.334550.641
8_W100_F0.334540.641
22_S110_K0.33350.639
8_W98_A0.333360.639
71_S76_V0.331740.636
14_R19_A0.330130.633
39_W48_Y0.324950.623
10_E67_Q0.324320.622
8_W12_F0.321960.617
28_F32_G0.318570.611
11_A20_L0.318520.610
68_V75_A0.317380.608
19_A23_L0.314370.602
26_D110_K0.308880.592
13_E58_P0.304190.583
9_I81_F0.303030.581
24_F111_I0.301120.577
9_I63_F0.301050.577
48_Y52_D0.29990.575
58_P84_R0.296570.568
12_F49_F0.296280.568
30_F49_F0.295680.567
56_F85_F0.291750.559
73_D105_E0.289440.555
8_W30_F0.28630.549
101_V112_V0.286260.549
20_L24_F0.284690.546
30_F45_I0.284010.544
71_S75_A0.283410.543
104_K107_G0.280880.538
72_G75_A0.278490.534
32_G81_F0.277880.533
77_V98_A0.27730.531
103_R113_H0.276380.530
65_D78_T0.273320.524
26_D43_E0.272270.522
62_E84_R0.272060.521
81_F100_F0.271960.521
84_R91_E0.271370.520
5_L79_G0.271360.520
28_F42_R0.270690.519
17_I20_L0.270420.518
66_V70_V0.269540.517
Legend: The value of the raw score is the function of the learning procedure, L2 normalization and APC (entropic) correction. These are to be used for relative ranking only.
HHsearch Results:
Top (length/2) GREMLIN results overlayed on top 10 PDB hits:

Legend: The grey circles underneath are pdb residue contacts (min distance < 5 Angstroms). The coloring of these circles is based on HHsearch results which uses the overall probability, per-site alignment prob and agreement of top hits weighted by HHsearch score (Note we only consider monomeric contacts, there might be homo-oligomeric contacts in the pdb that are not shown.)
PDB Cov Prob HH_delta
3f7sA0.991799.60.031
3h51A0.991799.50.094
3bb9A0.950499.50.114
2ux0A199.50.125
3gwrA0.983599.50.13
3hx8A0.983599.50.139
2f86B0.983599.40.159
3cnxA0.991799.40.165
3soyA0.983599.40.165
2gxfA0.991799.40.183

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